I am new user to do bioinformatic analysis and know a little about python. Right now, I succeed adding bowtie2- human genome index, and bowtie2 can recognize this built-in genome, however tophat2 can not recognize it.I do not know how to make a path to fix this. Would you like showing me steps in detail? Thank you very much!

Thank you very much for your help. I installed data_manager_bowtie2_index_builder before. I used this tool to add bowtie2 human reference index. Bowtie2 software can recognize this index well, however tophat2 can not did this. I also re-install data_manager_bowtie2_index_builder again. It is still no any change. Would you like to help me thinking about it again. Thank you very much in advance!